Working with Predicted Alignment Error Matrices in Jalview

Predicted Alignment Error (PAE) matrices are produced by deep-learning based 3D-structure prediction pipelines such as AlphaFold. They reflect how reliably two parts of a model have been positioned in space, by giving for each residue the likely error (in Ångstroms) between that residue and every other modelled position the pair of residues' real relative position, if the model and real 3D structure were superimposed at that residue.

Jalview visualises PAE matrices as an alignment annotation track, shaded from dark green to white, similar to the encoding used on the EBI-AlphaFold website (see O04090 3D model at EBI-AlphaFoldDB).

Importing PAE Matrices

Jalview retrieves PAE matrices when importing predicted 3D structures from the EBI-AlphaFold database via Jalview's structure chooser GUI. If you have produced your own models and accompanying PAE matrices using a pipeline such as ColabFold, then you can load them both together via the Load PDB File dropdown menu in the 3D structure chooser. in a supported PAE format.

The Command Line Interface also provides a options for importing PAE matrices along side models, enabling the automated production of alignment figures annotated with PAE matrices and PLDDT scores.

Showing PAE Matrix Annotations

When viewing 3D structures from the EBI-AlphaFold database or local 3D structures with an associated PAE file, the PAE is imported as Reference Annotation, which is not always automatically added to the alignment view.

To show the PAE, right click the sequence and locate the 'Add Reference Annotation' entry in the Sequence ID submenu, or select all sequences and locate the option in the Selection submenu. You can do this in any alignment window (or view) where a sequence with associated PAE data appears.

Support for visualision and analysis of predicted alignment error matrices was added in Jalview 2.11.3.